Creating Groups

  1. For sequences in the alignment window (eg PF03460 from PFAM (Seed) database), clear any selections using the [ESC] key.

  2. To create a group from the selected region, place the mouse cursor on a residue then click and drag the mouse to the bottom-right. As you drag, a red box will ‘rubber band’ out to show the selection, release and a red box outlines the selected region.

  3. Place the mouse inside the selection, right click to open a context menu and select Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour $\Rightarrow$ Percentage Identity. This turns the selected region into a group and colour it accordingly.

  4. With the group selected, hold down [CTRL] ([CMD] on Mac) and use the mouse to click on Sequence ID names to select and deselect sequences in the group. Note how the group expands to include newly selected sequences and the colouring changes.

  5. Another way to resize the group is simply to use the mouse to click and drag the right-hand edge of the selected group.

  6. The current selection can be exported and saved, placing mouse inside the group and right-click to open the context menu and select Selection $\Rightarrow$ Output to Textbox… and pick an output format such as BLC. In the Alignment output window that opens, manually edit the alignment before clicking the New Window button. This opens the edited alignment in a new alignment window.

For more information on this topic go to section 2.2 of the Jalview manual.
 This exercise can be viewed in the Selecting and exporting groups of residues in sequence alignments video.